Introduction | Installation | Quick Start | Case Study | Prepare DESeqDataSet | Filter Genes | Estimate Size Factors and Dispersions, Fit Negative Binomial Models, and Perform Wald Test | Estimate Latent Factors | Prepare Inputs | Identify Number of Factors to Estimate | Estimate Factors | Append Latent Factors to colData | Re-Fit Negative Binomial Models and Perform Wald Tests with Surrogate Variables | Extract Results | Display Results | sessionInfo()
Package: FieldEffectCrc 1.22.0
Christopher Dampier
FieldEffectCrc: Tumor, tumor-adjacent normal, and healthy colorectal transcriptomes as SummarizedExperiment objects
Processed RNA-seq data for 1,139 human primary colorectal tissue samples across three phenotypes, including tumor, normal adjacent-to-tumor, and healthy, available as Synapse ID syn22237139 on synapse.org. Data have been parsed into SummarizedExperiment objects available via ExperimentHub to facilitate reproducibility and extension of results from Dampier et al. (PMCID: PMC7386360, PMID: 32764205).
Authors:
FieldEffectCrc_1.22.0.tar.gz
FieldEffectCrc_1.22.0.tar.gz(r-4.7-any)FieldEffectCrc_1.22.0.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
FieldEffectCrc/json (API)
| # Install 'FieldEffectCrc' in R: |
| install.packages('FieldEffectCrc', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:FieldEffectCrc-1.23.0(data/experiment 3.24)FieldEffectCrc-1.22.0(data/experiment 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
experimentdatareproducibleresearchtissuehomo_sapiens_datacoloncancerdatarnaseqdataexpressiondataexperimenthubsequencingdatadatapkg
Last updated from:0331dcc408 (on RELEASE_3_23). Checks:1 ERROR, 3 OK. Indexed: no.
This is a data package. Data packages may be large and do not get checked across all platforms.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 145 | ||
| linux-devel | OK | 432 | ||
| source / vignettes | OK | 318 | ||
| linux-release | OK | 398 |
Exports:cohort A from Dampier et al.cohort B from Dampier et al.cohort C from Dampier et al.make_txireorder_assays
Dependencies:abindAnnotationDbiAnnotationHubaskpassbase64encBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocManagerBiocParallelBiocStyleBiocVersionBiostringsbitbit64blobbookdownbslibcachemclicodetoolscpp11crayoncurlDBIdbplyrDelayedArrayDESeq2digestdplyrevaluateExperimentHubfarverfastmapfilelockfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomicRangesggplot2gluegtablehighrhtmltoolshttrhttr2IRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelifecyclelocfitmagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigpngpurrrR6rappdirsRColorBrewerRcppRcppArmadillorlangrmarkdownRSQLiteRUnitS4ArraysS4VectorsS7sassscalesSeqinfosnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Tumor, tumor-adjacent normal, and healthy colorectal transcriptomes available as a 'SummarizedExperiment' object | FieldEffectCrc-package FieldEffectCrc |
| cohort A from Dampier et al. | cohort A from Dampier et al. cohort-A cohortA |
| cohort B from Dampier et al. | cohort B from Dampier et al. cohort-B cohortB |
| cohort C from Dampier et al. | cohort C from Dampier et al. cohort-C cohortC |
| Make a 'tximport'-style list object from a 'SummarizedExperiment' | make_txi |
| Re-order the elements of the 'assays' slot of a 'SummarizedExperiment' object to make counts the first element | reorder_assays |
